X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2FUtil.java;h=f033bf01d616434001a3225f990d5d25ac478627;hb=a966c1a63f4365f34a0567514dee6d1bc4d3af91;hp=8d778644f8f3e5f9431a4649c5c398e5c76f6763;hpb=c97b1954611988b2b1d2e9aeec6e4b0696a0ab66;p=jabaws.git

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index 8d77864..f033bf0 100644
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -19,6 +19,7 @@
 package compbio.runner;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -30,6 +31,7 @@ import org.apache.log4j.Logger;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAstruct;
 import compbio.data.sequence.Score;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
@@ -130,5 +132,41 @@ public final class Util {
 							+ e.getLocalizedMessage(), e);
 		}
 	}
+	
+	public static void writeClustalInput(List<FastaSequence> sequences,
+			ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {
+		
+		try {
+			File filein = new File(exec.getInput());
+			FileOutputStream fout = new FileOutputStream(filein);
+			log.debug("File path: " + filein.getAbsolutePath());
+			SequenceUtil.writeClustal(fout, sequences, gapChar);
+			fout.close();
+		} catch (IOException e) {
+			log.error("IOException while writing input file into the disk: "
+					+ e.getLocalizedMessage(), e);
+			throw new JobSubmissionException(
+					"We are sorry but JABAWS server seems to have a problem! "
+						+ e.getLocalizedMessage(), e);
+		}
+	}
+	
+	public static final RNAstruct readRNAStructFile(String workDirectory,
+			String structFile) throws IOException, FileNotFoundException {
+		assert !compbio.util.Util.isEmpty(workDirectory);
+		assert !compbio.util.Util.isEmpty(structFile);
+		File sfile = new File(compbio.engine.client.Util.getFullPath(
+				workDirectory, structFile));
+		log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
+		if(!(sfile.exists() && sfile.length() > 0)) {
+			throw new FileNotFoundException("Result for the jobId "
+					+ workDirectory + "with file name " + structFile
+					+ " is not found!");
+		}
+		return compbio.data.sequence.SequenceUtil.readRNAalifoldResults(
+				new FileInputStream(sfile));
+	}
+	
+	
 
 }